Special

MmuINT0139759 @ mm9

Intron Retention

Gene
ENSMUSG00000034810 | Scn7a
Description
sodium channel, voltage-gated, type VII, alpha [Source:MGI Symbol;Acc:MGI:102965]
Coordinates
chr2:66532867-66536044:-
Coord C1 exon
chr2:66535610-66536044
Coord A exon
chr2:66532973-66535609
Coord C2 exon
chr2:66532867-66532972
Length
2637 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
GGGGCTATAACTTTTTCTAGAAA
3' ss Score
3.12
Exon sequences
Seq C1 exon
ATACTTTACCTCTTTGTGACATTGGTGAGCTCTTTCAGTTACTATGATGCTACATCGGAAGTGAACAAAGAAGCCAAAAACCTTCAGCTTGCCATGGCAAGGATAAAGTCGGGAATAAACTCCATGCTTCTTAAATTAATGTGCACAGAAAGAAGTGTTCCTACAGAAGCAACAGACCAAATATGTGATCCAAGTGTTAAAGAGAATATTTCTGGCCATACTCTTTCTGAACTGAGCAACACCCAAACTTTCCTCAGATATAAGGACCAGAGCAGCAGCACTGAGAAAACTCCAGTGACTGAATCTGAGAGTCAATCTCTGATTGCTAGTCCCAGTGCCTCTGAAACTGTGCCGATTGCTTCAGGAGAATCTGATATAGAAAATCTGGATAACAAGGAGACTCGGAGCAAGTCTGGGAATGGAGGCAGTAAAGAG
Seq A exon
GTAAGGTGTTCAATTATATTCATTTTTTTTTTAGTGTGGATTTGTGGTTTTGTTCAAAAGAAATAAGTCAATGCTGATGTTATAGAGTTAAATTGCACATTTGATTTTAAATCCACCTTACCTAACTACTGGGTTCCATGGTTTTGACCAAATTATGTAAGTGCCCAAGCTTTTGTTTCTTTATCCGAAAATGAAGATATATTTCTTTTAGAGGGAAGAAGTAAGAGAAATAGTAGCGACTTTGCCTAGAGTAAAGTGATATTCTGGAGATATAAGATGGTATAATTGTGGTGATGAAAATCATTTTTAAAGCACATACATACTTTTGTAAAACATCAAGGTATATGATTGGGAGATGTGGATTCCTTGTGTATTATCATCTTCAAGATGTGAGAATAGCTTAAAAGAGTAGGGCATGATTCTTTCTTGCTTGTTAAGAATGAAAGTTTAGTCCATTCATGTCTACCATATATATAAATTAAAGTACATTAAGACTAAAAAAAATAATAAAGTCACTAGTTTGAATTGTGACTAGTTGGTAATTTTATAAATTCCTGACTTAGAAAAAAAATAGCACACACATTAAAAAGTTGTTGTTCACTTAGCTTCTGAAATATTTAGTGTTGTATCCTTTCCACTTAGAAATAACTTAATGCATTATCAAAAGGTAAAGTTCAGTAAGAGCCATTCTTACACAGAGCACTATGTGCTGTATCAGCTTGAAGCTCTGAGTCTTATTGGGCATCATCTCAGGTCAGTCTAAGGCCCCAGAGAAGGACAGATTGCAGCTTCTCCATGTCCCCATCATGCCTGGCAGCCCTTTCATCAAACCTCTGCTGGTTAGGCATATGTGTTCTATTATAATGCTTCAAATGTGTCTTCTGATGCAAGTTCAGGATGAGTAATCAGTAGCCCCTAAACTTCCCTCTGAGCACATCAATATTGTTGGCTTTCTTTATCCTTAATCACAAGATGATTGCAATCCCTGTTCCTCAAACATTCACACGTATCTTTCTTCTCTGAACACTTGGTTTCCATGCAGCTCTACATAGAACTGCTGTATAGCATAGTAAATAGAACCAGGTTTTCATCAGAAAATCTTAATAATATCATTAGAAAGTCTAAAGCACAAAATACAGAATAAAAGAACAATGTAAAATAACTGTAAATATTGAATTTTAGAGTCTGTCAATAATATTGTATGCTTATTTAAGCCTATATTTGGATAAATAATTTCTCAAAGATTTATTCCTTTACATATATGCTAGGTTATATATTTAATTAGTCATTTTGTCGATTATGTAGTCCAAGAATATTTAGTGTACCTTGGTCTAAAAATACAACTAGTAAAGAATGAAAAACACTAATTTAAGAAATATAGTTTCATTTGTATACATTTATCCTTCCTTTGAAATATTATGTATGTACATAAGACTGATCAAACTACTCATCAAGTTGTGAAACTTTTAAAAAATATAGTGTTATATCACAATACATTTTTCATGACATTCTGTAACCTACCAAAGTAAATTATAATTTATATTTTGAGCTCTATGTGATATAATTAAAAGTAAAGCTGTCGAAGTATCATATCAATATCATATGGACAAGTGTTTGATAATATGTATAGCAAGTATGCAAATATTTATATATATATATATACATACATATATATACATACATACATATATATATATATACATATATATATATAATATCTTTCTGCCCACTTTGTTTCTTTGCTCAAGCAACACATTATACTGAAATTACAAATGAATGTGTAAAAACTAAAGCAAAGAAAGCATTCTATTGTACTGATTGTGCATAAGATTACAAGGAATGACCAAGTATCGATAAGTTCTTTTTCCAAAATCTATCTAAATAATCCTGCAGTAATAACATTTCTATATACTCATTGTGATTTGTCTAGATTAGGAAATATCTTTTGGTGCTACTGGCTTATAGGACTCTGGTGCATTTAAAGGATAGTACATGTTTATGTCCATTTCAAAGTCAAGTAAACCAAGTGTCTACCACATGTACAAAGCGATAAACACTTTGACTCAGCAGCCTTGGGCTCTGTCATGGGCAAGTGCAAATGAAGAACCACTCTCTCTCCACGATCTTCCTATATGGCTTTATCCACTTGCCCCACTCTGTCGAGAGACCTCTTCTGTGTGTGCTTCTCTTTTCATATCGTTATAACATCATGTACAAAGTTGACAAGCACAAAACTATCTGGATTGGATTAAGCAGTTACAATGAAATTTATTTTCCACTCAGTGGTAGAATGAATTATTGTGATGTATCTATCTAATTAAAACAACACATATAAGTCCCATGTGAATTGTCTTAAAATTCATAACATAATTATTTTATAAACAATAAGTAAAGTCCTTTATACCTAAACTTTAATTTTATTCAAAGTTATTTTCACTTAAGTATTTCAAAGTAACATATAAAGCAAATATATACATAATGAATTTCATTTCAGGTCAGCCACAACTACTTTAAAATCTTTTAACTTTGATAATATTTCTTTTGTATATCATATTTACTTATGAAAATGAAACAAACCCACAATAATCAAGTTAAACATTGACCGTAACTTTTTGTTGGGGCTATAACTTTTTCTAG
Seq C2 exon
AAAATGAAGCAGTCTAGCTCATCTGAGTGCAGCACAGTTGATATCGCTATTTCTGAAGAAGAAGAAATGGTCTATGAACATGAAAAGTCAAAGCTTCATAAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034810-Scn7a:NM_009135:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.441 A=NA C2=0.306
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0052026=Ion_trans=PD(4.2=5.5),PF065128=Na_trans_assoc=PU(60.3=84.8)

							
A:
NA

							
C2:
PF065128=Na_trans_assoc=FE(17.2=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000042405





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:166429275-166432317 
ALTERNATIVE
HsaINT0145924
(SCN7A)
Human
(hg19)
chr2:167285785-167288827 
ALTERNATIVE
HsaINT0145924
(SCN7A)
Rat
(rn6)
chr3:52796996-52799620 
LOW PSI
RnoINT0131670
(Scn7a)
Cow
(bosTau6)
chr2:29972707-29975730 
LOW PSI
BtaINT0129500
(SCN7A)
Chicken
(galGal4)
chr7:19122531-19123611 
LOW PSI
GgaINT0047673
(SCN1A)
Chicken
(galGal3)
chr7:21098928-21100008 
LOW PSI
GgaINT0047673
(E1C4S3_CHICK)
Zebrafish
(danRer10)
chr6:39413218-39420432 
LOW PSI
DreINT0131565
(scn8ab)
Zebrafish
(danRer10)
chr9:50230665-50241583 
LOW PSI
DreINT0131420
(scn1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






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